IB Biology 2015

1. 5.4 Cladistics
Essential idea: The ancestry of groups of species can be
deduced by comparing their base or amino acid sequences.

3. Understandings
Statement Guidance
5.4.U1 A clade is a group of organisms that have evolved from a common
ancestor.
5.4.U2 Evidence for which species are part of a clade can be obtained from
the base sequences of a gene or the corresponding amino acid
sequence of a protein.
5.4.U3 Sequence differences accumulate gradually so there is a positive
correlation between the number of differences between two species
and the time since they diverged from a common ancestor.
5.4.U4 Traits can be analogous or homologous.
5.4.U5 Cladograms are tree diagrams that show the most probable sequence
of divergence in clades.
5.4. U6 Evidence from cladistics has shown that classifications of some groups
based on structure did not correspond with the evolutionary origins
of a group or species.

4. Applications and Skills
Statement Guidance
5.4.A1 Cladograms including humans and other primates.
5.4.A2 Reclassification of the figwort family using evidence from
cladistics.
5.4 S.1 Analysis of cladograms to deduce evolutionary relationships.

5. 5.4.1 A Clade is a group of organisms that have
evolved from a common ancestor
• Cladistics (From the
ancient Greek for
"branch") is a method
of classifying species
of organisms into
groups called clades,
which consist of an
ancestor organism
and all its
descendants (and
nothing else).

6. 5.4.1 A Clade is a group of organisms that have
evolved from a common ancestor
http://upload.wikimedia.org/wikipedia/commons/6/6b/Lutjanus_kasmira_school.jpg

7. http://upload.wikimedia.org/wikipedia/commons/2/2b/Tiktaalik_roseae_life_restor.jpg
5.4.1 A Clade is a group of organisms that have
evolved from a common ancestor
Tiktaalik
• Represents the evolutionary transition
from fish to amphibians. And as such the
common ancestor to every animal in the
Clade after the fish.

8. 5.4.1 A Clade is a group of organisms that have
evolved from a common ancestor
http://upload.wikimedia.org/wikipedia/commons/1/19/Caerulea3_crop.jpg

9. 5.4.1 A Clade is a group of organisms that have
evolved from a common ancestor
http://upload.wikimedia.org/wikipedia/commons/d/dc/Furcifer_pardalis_-Z%C3%BCrich_Zoo-8a.jpg

10. Archaeopteryx is a famous example transitional fossils – it gives evidence for the evolution of
birds from reptiles like dinosaurs.
http://commons.wikimedia.org/wiki/File:Archaeopteryx_lithographica_%28Berlin_specimen%29.jpg
http://commons.wikimedia.org/wiki/File:Archaeopteryx_NT.jpg
Bird features:
• feathers
Dinosaur features include:
• jaws with sharp teeth
• three fingers with claws
• long bony tail
5.4.1 A Clade is a group of organisms that have
evolved from a common ancestor

11. Likewise, birds share the
common characteristic of
feathers
They too form a clade
5.4.1 A Clade is a group of organisms that have
evolved from a common ancestor
http://upload.wikimedia.org/wikipedia/commons/0/03/Mountain_Bluebird.jpg

12. Mammals have the unique homologous
characteristic of producing milk
They form a clade
5.4.1 A Clade is a group of organisms that have
evolved from a common ancestor
http://images.nationalgeographic.com/wpf/media-
live/photos/000/334/cache/freshwater-mammals-hippo_33402_600x450.jpg

13. For example, Fish,
Amphibians, Reptiles,
Birds, Mammals, and
all descendants from
a common ancestor to
form a clade
5.4.1 A Clade is a group of organisms that have
evolved from a common ancestor

14. Characteristics change over time,
thus the amount of change can
help determine relationships
Groups of organisms are descended
from a common ancestor
There is a branching pattern in the
evolution of species and when a
split occurs, two distinct species
eventuate (SPECIATION!)

15. http://bridgeurl.com/xrmmmk/all
Vertebrate
Hair Shelled
eggs
Amniotic Egg
Four Limbs
Bony Skeleton
Each clade
is determined by
common characteristics
of its members that are
different from that of the
other species from which
it has diverged

16. Morphology (or there outward appearance) is only
one part of the story in cladistics. DNA and the
amino acids they code for are the primary basis for
grouping organisms into clades and determining
likely paths of evolutionary descent
Ex: Crocodiles are more closely related to birds than lizards…
5.4.2 Evidence for which species are part of a clade can be obtained
from the base sequences of a gene or the corresponding amino acid
sequence of a protein.

17. All known organisms use
DNA as genetic material
The genetic code is
universal. Gene
sequences inserted in
different organisms
express the same proteins
5.4.2 Evidence for which species are part of a clade can be obtained
from the base sequences of a gene or the corresponding amino acid
sequence of a protein.

18. The same 20 amino
acids are used to make
all proteins
http://commons.wikimedia.org/wiki/File:Protein_primary_structure.svg

21. Taking the example of the protein cytochrome c.
It is not identical in all species because single
point mutations in the DNA that codes for it can
lead to different amino acids making up the
protein.
Both humans and chimpanzees have identical
cytochrome c molecules, while rhesus monkeys
share all but one of the amino acids.
This suggests that humans and chimpanzees are
more closely related to each other than to rhesus
monkeys.
I didn’t want to be
closely related to
stinking humans
anyway!
http://www.flickr.com/photos/stuffinhergoose/571672799
5.4.2 Evidence for which species are part of a clade can be obtained
from the base sequences of a gene or the corresponding amino acid
sequence of a protein.

22. Molecular biology
Protein and DNA Structures Reveal Associations Between
Organisms
• Nuclear DNA code is highly conserved across phyla – although there
are variations, there are no alternate codes
• Nuclear DNA can be used to show associations between organisms
when comparing very long suspected evolutionary times
• Ribosomal RNA and mitochondrial DNA & RNA more useful when
comparing shorter evolutionary times… they are inherently more
variable over time because they are subjected to fewer selection
pressures.
• Small changes are seen in the DNA code between closely related
species.
• Monkeys, apes, and humans clearly have common ancestry
5.4.3 Sequence differences accumulate gradually so there is a positive
correlation between the number of differences between two species
and the time since they diverged from a common ancestor.

23. Base Sequence Comparisons
• Divergence (difference) in
nucleotide base sequence
allows us to draw
relationships between
different organisms.
• Here, differences in
nucleotide base sequence
of humans and other
primates compared
• Chimps closest, spider
monkeys most dissimilar
5.4.3 Sequence differences accumulate gradually so there is a positive
correlation between the number of differences between two species
and the time since they diverged from a common ancestor.

24. Molecular Clocks
• DNA undergoes relatively
steady rates of mutation
over time
• More divergence in structure
is assumed to mean more
time has passed
• Changes in homologous DNA
from different species allows
biologists to construct
molecular clocks based on
the rates of change in known
and homologous DNA
• This can aid in the dating of
branching points in the
evolutionary record
5.4.3 Sequence differences accumulate gradually so there is a positive
correlation between the number of differences between two species
and the time since they diverged from a common ancestor.

25. The assumption is that these changes occur at a regular rate.
(which may not always be the case)
Therefore if species A had 5 differences from species B and 10
differences from species C, then the lineages for A and C must
have split twice as long ago as for A and B
C B A
Time

26. spines
tendrils
succulent leaves
colored leaves
Homologous structures
leaves
needles
5.4 U.4 Traits can be analogous or homologous.

27. Analogous structures
• Separate evolution of
structures
similar functions
similar external form
different internal
structure &
development
different origin
no evolutionary
relationship
Solving a similar problem with a similar solution
http://upload.wikimedia.org/wikipedia/commons/5/5c/Male_-
_black_phase_-_short_tail_hawk.JPG
http://www.redorbit.com/media/uploads/2004/1
0/40_03aa91083d476b07bcc9228e134d6c56.jpg
Convergent evolution
5.4 U.4 Traits can be analogous or homologous.

28. Convergent evolution
• Fish: aquatic vertebrates
• Humpback Whale: aquatic mammals
similar adaptations to life in the sea
not closely related
5.4 U.4 Traits can be analogous or homologous.

29. 5.4 U.4 Traits can be analogous or homologous.

30. Convergent evolution
• Flight evolved in 3 separate
animal groups
– evolved similar “solution” to
similar “problems”
– analogous structures
http://upload.wikimedia.org/wikipedia/commons
/7/77/Big-eared-townsend-fledermaus.jpg
http://upload.wikimedia.org/wikipedia/commons/e/e0/
5.4 U.4 Traits can be analogous or homologous.

31. 5.4.5 Cladograms are tree diagrams that show the most
probable sequence of divergence in clades.
• These two cladograms are identical (although they don’t look it)
• The shape and the order of the terminal nodes does not matter.
• The only information to be gathered from the cladograms below is the order of
nesting of sister clades and the relative relatedness of species
http://commons.wikimedia.org/wiki/File:Identical_cladograms.svg

32. Human HumanChimp ChimpGorilla Gorilla
Root
Terminal nodes Sister clades: have a
common ancestor
Out group: Defines
the ancestral
characters
Nodes:
Common ancestors

34. http://www.studentsoftheworld.info/infopays/photos/PER/orig/lamas.jpg
5.4.6 Evidence from cladistics has shown that classification of some
groups based on structure did not correspond with the evolutionary
origins of a group or species.

35. http://www.scratchwireless.com/pad/wp-content/uploads/2015/02/SheepFlock.jpg
5.4.6 Evidence from cladistics has shown that classification of some
groups based on structure did not correspond with the evolutionary
origins of a group or species.

36. http://ianadamsphotography.com/news/wp-content/uploads/2014/12/Bactrian-Camels-the-Wilds.jpg
5.4.6 Evidence from cladistics has shown that classification of some
groups based on structure did not correspond with the evolutionary
origins of a group or species.

37. Evolutionary Links
Classification allows us to see evolutionary relationships. Organisms
that are grouped together share a lot of similar features (homologous
structures). These shared characteristics help us see how organisms
have evolved from a common ancestor. HOWEVER, morphology (or
there outward appearance) has its limitations in terms of evolutionary
classification and DNA/ Amino Acid evidence is now far more accurate
and trustworthy…
http://www.flickr.com/photos/doug88888/3458057235/http://www.flickr.com/photos/mrapplegate/2423991076/
e.g. Llamas were
originally compared to
sheep but a study of
their genetics later
placed them in the
camel family
5.4.6 Evidence from cladistics has shown that classification of some
groups based on structure did not correspond with the evolutionary
origins of a group or species.

38. This is part of a molecular phylogeny of all of the
living primates. It clearly shows chimpanzees (Pan)
as more closely related to humans than to gorillas.
It was made by comparing 34,927 base pairs
sequenced from 54 genes taken from each
of a single species in each genus.
5.4.7 Analyze cladograms including humans and other primates.

39. 5.4 S.1 Analyze cladograms to deduce evolutionary
relationships.
1
2
3
DCBA
Which two species
are most closely-
related by evolution?
Which node
represents the
earliest speciation /
divergence?
Which species is D
more closely related
to; A or B?

42. Characters Shark Frog Kangaroo Human
Vertebrae X X X X
Two pairs of limbs X X X
Mammary glands X X
Placenta X
1) Compile a table of the characters being compared
Modified from:
http://www.bu.edu/gk12/eric/cladogram.pdf

43. Vertebrae:
Shark
Two Pairs of
Limbs: Frog
Mammary
Glands:
Kangaroo
Placenta:
Human
2) Use the data to construct
a Venn diagram,
Start with the
characteristic
shared by all
taxa in the
biggest circle
and work
inwards

44. Shark Frog Kangaroo Human
Mammary Glands
Lungs
Vertebrae
Placenta
3) Convert the Venn diagram into a cladogram

45. Characters Sponge Jellyfish Flatworm Earth-
worm
Snail Fruit fly Starfish Human
Cells with flagella X X X X X X X X
Symmetry X X X X X X X
Bilateral symmetry X X X X X X
Mesoderm X X X X X
Head develops first X X X
Anus develops first X X
Segmented body X X
Calcified shell X
Chitinous Exoskeleton X
Water Vascular system X
Vertebrae X
Another Example:

46. Cells with flagella: Sponge
Symmetry: Jellyfish
Bilateral symmetry: Flatworm
Mesoderm
Head develops first Anus develops first
Segmented Body:
Earthworm Calcified
Shell:
SnailChitinous
exoskeleton:
Fruit fly
Water
Vascular
system:
Starfish
Vertebrae:
Human
It should look
something
like this:
now make
the cladogram

47. Flagella
Mesoderm
Bilateral symmetry
Symmetry
Vertebrae
Anus develops first
Chitinous
shell
Head develops
first
Sponge StarfishFruit flySnail
Flat-
worm EarthwormJellyfish Human
Water
vascular
system
Calcified
shell
Segmented body
It should look something like this:
Some of the
characteristics in the
data table were unnecessary
for the construction of this
cladogram.
Can you identify them?

48. • Morphology was used to classify
the Figworts. Until recently,
Figworts were the 8th largest
family of angiosperms (flowering
plants). It grew from 16 genera
in 1789 to 275 genera
• Flowers of plants in Figworts
tend to be pretty uniform in
their appearance, typically
having corollas with bilateral
symmetry
• Taxonomists recently examined
chloroplast genes and found the
5000 figwort species should be
split into 5 different clades
rather than just one.
5.4 A.1Discuss reclassification of the figwort family using evidence from
cladistics.
http://www.jardinexotiqueroscoff.com/site/uploads/pictures/plante
/800x800/scrophulariaceae-diascia-rigescens-13.jpg

49. 5.4 A.1Discuss reclassification of the figwort family using
evidence from cladistics.
http://upload.wikimedia.org/wikipedia/commons/2/2e/2007_Hippuris_vulgaris.jpg
Hippuris vulgaris (out)

50. 5.4 A.1Discuss reclassification of the figwort family using
evidence from cladistics.
http://upload.wikimedia.org/wikipedia/commons/4/40/Castilleja_angustifolia_1.jpg
Applegate Indian paintbrush (out)

51. 5.4 A.1Discuss reclassification of the figwort family using
evidence from cladistics.
Snapdragon (out)

52. • Botanists in the 18th and 19th
centuries used plant taxonomy to
separate out groups.
• Now with the use of modern
techniques, less than half of the
original species remain in the
Figwort family; now only the 36th
largest among angiosperms
• Reclassification was helpful since
old Figwort family was too large
and dissimilar to be a helpful
grouping
• We should consider ourselves
fortunate to be a part of what is
one of the eras of greatest
advancement in the field it is a
tremendous age of discovery
No longer a
Figwort. Sad